From 630ae1c67e683e05b4276c48c2ad5575880eacc9 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Thu, 7 Jul 2011 04:07:56 +0000
Subject: [PATCH] bug fix in chronopl()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@164 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 DESCRIPTION  |  2 +-
 NEWS         |  3 +++
 R/chronopl.R | 16 +++++++++-------
 3 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a45a55b..4ea8236 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.7-3
-Date: 2011-06-22
+Date: 2011-07-04
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Klaus Schliep, Korbinian Strimmer, Damien de Vienne
 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
diff --git a/NEWS b/NEWS
index a3aa8c9..9e66a45 100644
--- a/NEWS
+++ b/NEWS
@@ -18,6 +18,9 @@ BUG FIXES
       process when alpha = 0 to avoid division by zero. The option
       'linear' has been removed.
 
+    o Cross-validation in chronopl() did not work when 'age.max' was
+      used.
+
 
 
 		CHANGES IN APE VERSION 2.7-2
diff --git a/R/chronopl.R b/R/chronopl.R
index 570fa26..0e72a3f 100644
--- a/R/chronopl.R
+++ b/R/chronopl.R
@@ -1,8 +1,8 @@
-## chronopl.R (2009-07-06)
+## chronopl.R (2011-07-04)
 
 ##   Molecular Dating With Penalized Likelihood
 
-## Copyright 2005-2009 Emmanuel Paradis
+## Copyright 2005-2011 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -80,6 +80,9 @@ chronopl <-
     ratio <- age.min[1]/ini.time[node[1]]
     ini.time <- ini.time*ratio
 
+    ## because if (!is.null(age.max)), 'node' is modified, so we copy it in case CV = TRUE:
+    node.bak <- node
+
     if (length(node) > 1) {
         ini.time[node] <- age.min
         real.edge.length <- ini.time[e[, 1]] - ini.time[e[, 2]]
@@ -94,12 +97,12 @@ chronopl <-
                     ini.time[e[i, 1]] <- ini.time[e[1, 1]] + 2 * real.edge.length[i]
                     next
                 }
-                browser()
+                ##browser()
                 ini.time[e[i, 2]] <- ini.time[e[1, 2]] - real.edge.length[i]
                 ini.time[e[i, 1]] <- ini.time[e[1, 1]] + real.edge.length[i]
             }
             real.edge.length <- ini.time[e[, 1]] - ini.time[e[, 2]]
-            print(min(real.edge.length))
+            ##print(min(real.edge.length))
         }
     }
     ## `unknown.ages' will contain the index of the nodes of unknown age:
@@ -198,7 +201,7 @@ chronopl <-
     if (CV) ophy <- phy
     phy$edge.length <- age[e[, 1]] - age[e[, 2]]
     if (CV) attr(phy, "D2") <-
-        chronopl.cv(ophy, lambda, age.min, age.max, node,
+        chronopl.cv(ophy, lambda, age.min, age.max, node.bak,
                     n, S, tol, eval.max, iter.max, ...)
     phy
 }
@@ -214,9 +217,8 @@ chronopl.cv <- function(ophy, lambda, age.min, age.max, nodes,
     BT <- branching.times(ophy)
     D2 <- numeric(n)
 
-    cat("  dropping tip")
     for (i in 1:n) {
-        cat(" ", i, sep = "")
+        cat("\r  dropping tip ", i, " / ", n, sep = "")
         tr <- drop.tip(ophy, i)
         j <- which(ophy$edge[, 2] == i)
         if (ophy$edge[j, 1] %in% nodes) {
-- 
2.39.2